Chapter 9 Discovery of the Double Helix

Who was the main founder of the alpha helix structure

According to Dr. V:

The main founder was Rosalind Franklin

Rosalind Franklin and Maurice Wilkins

scientist who generated x-ray diffraction and crystallizing DNA

--------------------------------

DISCOVERIES:

- they discovered that DNA was double stranded

- discovered the actual distance of the base pairs from the sugars within a DNA strand based upon the x-ray diffraction experiment

Rosalind Franklin (conclusion)

the diffraction pattern from her experiments suggested several structural features of DNA were:

- helical

- more than one strand

- 10 base pairs per complete turn

James Watson and Francis Crick

Scientists who discovered the structure of DNA

--------------------------------

According to Dr. V they both stole the idea from Rosalind Franklin and got all the credit.

Linus Pauling

proposed that regions of protein can fold into a secondary structure (alpha-helix)

--------------------------------

- was discovered in a similar scenario as Rosalind Franklin by using x-ray diffraction but this time studying the wet fibers of DNA

Erwin Chargaff (Chargaff's Rule)

discovered that A=T and G=C by analyzing base composition of DNA isolated from many different species

--------------------------------

DISCOVERY:

- based of his data he came to the conclusion that the ratios between complementaries are the same between A-T and C-G

Erwin Chargaff (experiment)

1. For each type of cell chromosomal material was extracted either by using, high salt, detergent, or mild alkali treatment

--------------------------------

2. Removal of protein

--------------------------------

3. Hydrolyze the DNA to release the bases from the DNA strands

- treated genomic DNA with strong acid (to break convalent bonds between sugars and bases)

Basic rule of thumb for Cargaff's rule

- Each base pair ALWAYS has 3 rings (purine + pyrimidine)

- the distance between A=T to G=C is always 3.4 nm

B-form DNA

- 10 base pairs per turn

- 3.4 nm per turn

- the two strands are antiparallel

- is the most common structure

- is almost always has a 90-degree angle

- dsDNA (double-stranded)

- right-handed alpha-helix

- has a deep indentation called a "Major and Minor Groove"

antiparallel strands

Strands parallel to each other going in opposite directions

--------------------------------

- 3'-5' and 5'-3'

--------------------------------

HINT: legit just think the opposite of

right handed alpha helix (B-form DNA)

spins counter-clockwise and is the most common structure

minor groove

A smaller groove that spirals around the DNA double helix.

--------------------------------

FUNCTION:

- provides a location where a protein can bind to a particular sequence of bases and affect gene expression

major groove

a larger groove that spirals around the DNA double helix

--------------------------------

FUNCTION:

- provides a location where a protein can bind to a particular sequence of bases and affect gene expression

Z-form DNA

- dsDNA

- left-handed alpha helix

- 12 base pairs per turn

- contains NO major or minor groove

- in vitro vs in vivo sides

- alters purine/pyrimidine sequences

- plays a role in transcription and chromosome structure

left handed alpha helix (Z-form DNA)

spins clockwise

in vitro vs in vivo sides

in vitro = outside a living cell

in vivo = inside a living cell

--------------------------------

in vitro the Z DNA has a high salt condition (meaning it has a higher ionic strength) than in vivo

altering purine/pyrimidine sequences

the DNA strand continuously alternates between G and C due to high salt contractions

--------------------------------

EXAMPLE:

GCGCGCGCGCGC........

transcription and chromosome structure

Z. Form DNA is responsible for mRNA to be formed

- it can be recognized by cellular proteins

- can alter chromosome compaction

B vs Z DNA structure

B. DNA

- bases are perpendicular to the central axis (90 degrees)

--------------------------------

Z. DNA

- bases substantially tilted relative to central axis

- sugar-phosphate backbone has a zigzag pattern

DNA structure

double-stranded structure stabilized by:

- hydrogen bonding between complementary bases

- Base stacking

--------------------------------

FEATURES:

- antiparallel

- contain 2 asymmetrical grooves on the outside of the helix (major and minor)

--------------------------------

RECAP:

DNA uses thymine as a base

DNA uses deoxyribose with 2' H

Hydrogen bonding between complementary bases

A-T = 2 hydrogen bonds

--------------------------------

C-G= 3 hydrogen bonds

base stacking

bases are oriented so that the flattened regions are facing each other

triple helix (OREO)

HISTORY:

founded by Alexander Rich by forming DNA pieces that were made synthetically to synthesize the base structure

--------------------------------

SEQUENCE:

- T binds to AT pair in biological DNA

- C binds to CG pair in biological DNA

RNA structure

- "are usually" single-stranded

- are typically several hundred to thousand nucleotides in length

--------------------------------

RECAP:

- RNA uses Uracil as a base

- RNA uses Ribose with 2' OH

RNA synthesis

only one of the two strands of DNA is used as a template

why is RNA bad in alkaline solutions?

the bases can easily deprotonate the hydrogen from the hydroxyl group on the 2'-carbon atom

RNA base pairings rules

Secondary stucture if formed due to complementary base pairing.

A-U

C-G

--------------------------------

- allows for short regions to form a double helix

RNA double helices

is very uncommon

--------------------------------

FEATURES:

- are right-handed alpha helixes

- have the A form with 11 to 12 base pairs in turn

RNA secondary structures

The structures themselves are formed as signals to recruit/attract proteins

--------------------------------

TYPES OF STRUCTURES:

- Bulge loop

- Internal Loop

- Multibranched Loop

- Stem Loop

bulge loop

similar to stem-loop but no stem

internal loop

unpaired nucleotides on either side of the stem

- contains a loop with no pairings

Multibranched Loop

Crossed nucleotides

Stem loop RNA

strand folds back on itself

- contains a loop with no pairings

- contains a stem unlike a Bulge loop

- stem contains base pairs

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

non-template strand (coding strand)

the strand of DNA that is not transcribed into RNA during transcription